They're both honors, yes, but incredibly different in the implementation. A MacArthur is much more of an abstract honor ('You have done some great work, possibly in some field that can't even be named because it is so unique, so here is some money that we hope you will use to continue doing great work.'). Many MacArthur recipients would never in their lifetimes be eligible for a Nobel. (On the other hand, many Nobel laureates would never receive a MacArthur either).

A Nobel prize, by contrast, is only given in certain fields, which already constrains the way that it is perceived. With a MacArthur, you're not necessarily competing against others in your field, because you oftentimes don't have a field (what you do is so highly specialized that nobody else really comes close). Furthermore, the prize is a political tool as much as anything else nowadays. (Looking at many of the recent Nobel Peace Prize recipients, I think anybody would agree to that.) The MacArthur has much less political identification, even compared to the prizes for biology/chemistry. It's nice to be able to attach it to your name when convenient as it gets a little bit more respect, but it's hard to interpret it in a negative way (or to see a recipient of a MacArthur as somehow compromising his/her views -- remember that Stallman has rather weak opinions on money per se when it comes to freedom; one can have a FLOSS product that nevertheless generates money).

(And as for the awards, I agree - at this point in my life I would probably be satisfied with either one!)